16S sequencing data - cow milk samples

## `summarise()` has grouped output by 'timepoint', 'treatment'. You can override using the `.groups` argument.
## # A tibble: 16 × 6
## # Groups:   treatment [2]
##    treatment Cow_ID     `0`   `8`  `21`  `28`
##    <chr>     <chr>    <int> <int> <int> <int>
##  1 Control   4251 AG      1     1     1     1
##  2 Control   4251 ARD     1     1     1     1
##  3 Control   4330 ARD     1     1     1     1
##  4 Control   5303 ARD     1     1     1     1
##  5 Control   6201 AG      1     1     1     1
##  6 Control   6201 ARG     1     1     1     1
##  7 Control   6221 ARG     1     1     1     1
##  8 Control   6249 AG      1     1     1     1
##  9 Treated   4252 AD      1     1     1     1
## 10 Treated   4252 AG      1     1     1     1
## 11 Treated   4287 AG      1     1     1     1
## 12 Treated   5240 AD      1     1     1     1
## 13 Treated   5240 ARD     1     1     1     1
## 14 Treated   5250 AD      1     1     1     1
## 15 Treated   6261 ARD     1     1     1     1
## 16 Treated   7249 ARG     1     1     1     1

Treatments and timepoints

First, let’s look at phyla:

phylum treatment timepoint N avg_abund std
Firmicutes Control 28 8 0.2414 0.119
Firmicutes Control 21 8 0.2753 0.090
Firmicutes Control 8 8 0.3945 0.129
Firmicutes Control 0 8 0.4610 0.127
Proteobacteria Control 0 8 0.2176 0.104
Proteobacteria Control 8 8 0.2911 0.147
Proteobacteria Control 21 8 0.3559 0.111
Proteobacteria Control 28 8 0.4594 0.161
Actinobacteria Control 0 8 0.1225 0.059
Actinobacteria Control 8 8 0.1344 0.049
Actinobacteria Control 21 8 0.1785 0.029
Actinobacteria Control 28 8 0.1785 0.045
Bacteroidetes Control 28 8 0.0766 0.050
Bacteroidetes Control 21 8 0.1120 0.035
Bacteroidetes Control 8 8 0.1148 0.026
Bacteroidetes Control 0 8 0.1341 0.023
Firmicutes Treated 28 8 0.3689 0.108
Firmicutes Treated 8 8 0.3781 0.123
Firmicutes Treated 21 8 0.4007 0.147
Firmicutes Treated 0 8 0.4081 0.087
Proteobacteria Treated 21 8 0.2458 0.127
Proteobacteria Treated 0 8 0.2507 0.079
Proteobacteria Treated 8 8 0.2855 0.147
Proteobacteria Treated 28 8 0.3000 0.164
Actinobacteria Treated 21 8 0.1149 0.038
Actinobacteria Treated 0 8 0.1438 0.033
Actinobacteria Treated 28 8 0.1540 0.021
Actinobacteria Treated 8 8 0.1577 0.039
Bacteroidetes Treated 28 8 0.1135 0.044
Bacteroidetes Treated 8 8 0.1147 0.035
Bacteroidetes Treated 0 8 0.1308 0.021
Bacteroidetes Treated 21 8 0.1487 0.025

###boxplot abundances per timepoint and treatment

##Phyla

Treatments, all taxonomic levels

## 
##     2     3     4     5     6 
##  2048  4416 10496 24832 69120

A table of relative abundances (and standard deviations) per taxa and treatment:

level new_taxa treatment timepoint avg_abund std
class Clostridia Control 0 0.3587 0.158
class Gammaproteobacteria Control 28 0.3224 0.102
class Clostridia Treated 21 0.2907 0.161
class Clostridia Treated 0 0.2875 0.092
class Clostridia Control 8 0.2556 0.132
class Clostridia Treated 28 0.2478 0.086
class Clostridia Treated 8 0.2419 0.118
class Gammaproteobacteria Control 21 0.2209 0.068
class Gammaproteobacteria Treated 28 0.2116 0.113
class Gammaproteobacteria Control 8 0.1972 0.100
class Gammaproteobacteria Treated 0 0.1826 0.042
class Gammaproteobacteria Treated 8 0.1801 0.098
class Clostridia Control 21 0.1766 0.084
class Actinobacteria Control 28 0.1734 0.048
class Gammaproteobacteria Treated 21 0.1602 0.092
class Actinobacteria Control 21 0.1590 0.031
class Gammaproteobacteria Control 0 0.1545 0.067
class Bacteroidia Treated 21 0.1487 0.025
class Actinobacteria Treated 8 0.1444 0.037
class Clostridia Control 28 0.1438 0.102
class Actinobacteria Treated 28 0.1416 0.019
class Alphaproteobacteria Control 28 0.1358 0.068
class Bacteroidia Control 0 0.1341 0.023
class Actinobacteria Treated 0 0.1334 0.031
class Alphaproteobacteria Control 21 0.1331 0.050
class Bacteroidia Treated 0 0.1308 0.021
class Bacilli Control 8 0.1244 0.054
class Actinobacteria Control 8 0.1237 0.047
class Bacilli Treated 8 0.1227 0.032
class Bacteroidia Control 8 0.1148 0.026
class Bacteroidia Treated 8 0.1147 0.035
class Bacteroidia Treated 28 0.1135 0.044
class Bacteroidia Control 21 0.1120 0.035
class Actinobacteria Control 0 0.1109 0.060
class Bacilli Treated 28 0.1079 0.022
class Bacilli Treated 0 0.1061 0.013
class Actinobacteria Treated 21 0.1008 0.038
class Alphaproteobacteria Treated 8 0.0995 0.051
class Bacilli Treated 21 0.0952 0.036
class Alphaproteobacteria Control 8 0.0915 0.050
class Bacilli Control 21 0.0877 0.022
class Bacilli Control 0 0.0864 0.044
class Alphaproteobacteria Treated 28 0.0857 0.057
class Bacilli Control 28 0.0856 0.029
class Alphaproteobacteria Treated 21 0.0810 0.043
class Bacteroidia Control 28 0.0766 0.050
class Alphaproteobacteria Treated 0 0.0649 0.044
class Alphaproteobacteria Control 0 0.0599 0.042
class Erysipelotrichia Control 8 0.0104 0.004
family Ruminococcaceae Control 0 0.2013 0.119
family Ruminococcaceae Treated 21 0.1613 0.110
family Pseudomonadaceae Control 28 0.1409 0.065
family Ruminococcaceae Treated 0 0.1397 0.057
family Ruminococcaceae Control 8 0.1210 0.088
family Ruminococcaceae Treated 8 0.1189 0.067
family Ruminococcaceae Treated 28 0.1167 0.041
family Pseudomonadaceae Control 21 0.0825 0.045
family Ruminococcaceae Control 21 0.0813 0.051
family Propionibacteriaceae Control 28 0.0759 0.028
family Ruminococcaceae Control 28 0.0757 0.054
family Lachnospiraceae Control 0 0.0734 0.018
family Beijerinckiaceae Control 28 0.0675 0.032
family Pseudomonadaceae Treated 28 0.0672 0.071
family Pseudomonadaceae Control 8 0.0668 0.061
family Lachnospiraceae Treated 0 0.0626 0.023
family Lachnospiraceae Control 8 0.0598 0.019
family Pseudomonadaceae Treated 8 0.0593 0.055
family Lachnospiraceae Treated 21 0.0590 0.030
family Lachnospiraceae Treated 28 0.0582 0.023
family Lachnospiraceae Treated 8 0.0558 0.021
family Moraxellaceae Control 28 0.0522 0.012
family Halomonadaceae Control 28 0.0514 0.021
family Pseudomonadaceae Treated 0 0.0507 0.027
family Pseudomonadaceae Treated 21 0.0497 0.042
family Beijerinckiaceae Control 8 0.0459 0.037
family Moraxellaceae Treated 28 0.0456 0.010
family Pseudomonadaceae Control 0 0.0454 0.029
family Beijerinckiaceae Control 21 0.0453 0.022
family Propionibacteriaceae Treated 28 0.0445 0.021
family Moraxellaceae Treated 0 0.0441 0.011
family Staphylococcaceae Control 8 0.0438 0.048
family Prevotellaceae Treated 21 0.0427 0.018
family Beijerinckiaceae Treated 8 0.0424 0.029
family Lachnospiraceae Control 21 0.0423 0.015
family Staphylococcaceae Treated 8 0.0411 0.016
family Moraxellaceae Control 8 0.0405 0.014
family Propionibacteriaceae Control 21 0.0396 0.021
family Propionibacteriaceae Treated 0 0.0389 0.014
family Propionibacteriaceae Control 0 0.0379 0.026
family Propionibacteriaceae Control 8 0.0379 0.021
family Prevotellaceae Treated 0 0.0371 0.008
family Moraxellaceae Control 0 0.0369 0.020
family Prevotellaceae Control 8 0.0364 0.009
family Moraxellaceae Treated 8 0.0363 0.019
family Propionibacteriaceae Treated 8 0.0359 0.019
family Prevotellaceae Control 0 0.0354 0.007
family Micrococcaceae Treated 28 0.0352 0.014
family Micrococcaceae Control 28 0.0348 0.016
family Micrococcaceae Treated 0 0.0348 0.009
family Beijerinckiaceae Treated 28 0.0345 0.030
family Rikenellaceae Control 0 0.0345 0.014
family Moraxellaceae Control 21 0.0344 0.013
family Micrococcaceae Treated 8 0.0338 0.012
family Prevotellaceae Treated 28 0.0333 0.012
family Halomonadaceae Control 21 0.0329 0.015
family Rikenellaceae Treated 0 0.0329 0.013
family Halomonadaceae Control 8 0.0324 0.024
family Prevotellaceae Treated 8 0.0322 0.011
family Rikenellaceae Treated 21 0.0322 0.017
family Lachnospiraceae Control 28 0.0317 0.026
family Staphylococcaceae Control 28 0.0316 0.022
family Christensenellaceae Control 0 0.0312 0.025
family Rikenellaceae Treated 28 0.0311 0.014
family Halomonadaceae Treated 28 0.0303 0.021
family Streptococcaceae Control 8 0.0299 0.013
family Streptococcaceae Treated 28 0.0296 0.015
family Streptococcaceae Treated 0 0.0290 0.011
family Micrococcaceae Control 0 0.0287 0.018
family Micrococcaceae Control 8 0.0287 0.011
family Moraxellaceae Treated 21 0.0275 0.018
family Staphylococcaceae Treated 28 0.0273 0.013
family Prevotellaceae Control 28 0.0272 0.021
family Rhizobiaceae Control 28 0.0268 0.023
family Christensenellaceae Treated 0 0.0261 0.011
family Staphylococcaceae Control 21 0.0261 0.015
family Prevotellaceae Control 21 0.0260 0.010
family Halomonadaceae Treated 8 0.0258 0.019
family Rikenellaceae Control 8 0.0256 0.009
family Streptococcaceae Control 0 0.0256 0.017
family Sphingomonadaceae Control 21 0.0253 0.012
family Beijerinckiaceae Treated 21 0.0252 0.021
family Rhizobiaceae Control 21 0.0248 0.018
family Rikenellaceae Treated 8 0.0247 0.014
family Beijerinckiaceae Treated 0 0.0246 0.018
family Streptococcaceae Treated 8 0.0244 0.012
family Christensenellaceae Treated 21 0.0242 0.015
family Corynebacteriaceae Control 21 0.0239 0.014
family Micrococcaceae Control 21 0.0239 0.008
family Beijerinckiaceae Control 0 0.0236 0.017
family Micrococcaceae Treated 21 0.0235 0.018
family Propionibacteriaceae Treated 21 0.0234 0.016
family Burkholderiaceae Control 21 0.0230 0.011
family Christensenellaceae Control 8 0.0229 0.021
family Staphylococcaceae Treated 21 0.0228 0.012
family Halomonadaceae Treated 0 0.0226 0.007
family Streptococcaceae Treated 21 0.0226 0.018
family Staphylococcaceae Treated 0 0.0224 0.009
family Halomonadaceae Control 0 0.0217 0.010
family Halomonadaceae Treated 21 0.0216 0.015
family Corynebacteriaceae Treated 8 0.0214 0.009
family Corynebacteriaceae Control 8 0.0207 0.015
family Staphylococcaceae Control 0 0.0207 0.011
family Bacteroidaceae Control 0 0.0205 0.009
family Peptostreptococcaceae Treated 28 0.0204 0.005
family Christensenellaceae Treated 28 0.0202 0.008
family Corynebacteriaceae Control 28 0.0201 0.010
family Peptostreptococcaceae Treated 8 0.0197 0.007
family Corynebacteriaceae Treated 0 0.0194 0.005
family Corynebacteriaceae Treated 28 0.0190 0.007
family Rikenellaceae Control 28 0.0188 0.013
family Peptostreptococcaceae Treated 0 0.0187 0.004
family Sphingomonadaceae Treated 8 0.0182 0.013
family Streptococcaceae Control 28 0.0181 0.014
family Carnobacteriaceae Treated 0 0.0178 0.007
family Rhizobiaceae Treated 28 0.0174 0.016
family Rikenellaceae Control 21 0.0173 0.009
family Peptostreptococcaceae Control 21 0.0168 0.011
family Christensenellaceae Treated 8 0.0166 0.013
family Bacteroidaceae Treated 21 0.0165 0.010
family Burkholderiaceae Control 28 0.0165 0.009
family Bacteroidaceae Treated 0 0.0164 0.006
family Streptococcaceae Control 21 0.0161 0.010
family Bacillaceae Treated 8 0.0159 0.008
family Peptostreptococcaceae Control 8 0.0159 0.009
family Flavobacteriaceae Control 21 0.0156 0.011
family Nocardioidaceae Control 21 0.0154 0.010
family Sphingomonadaceae Treated 21 0.0154 0.016
family Corynebacteriaceae Control 0 0.0153 0.010
family Rhizobiaceae Treated 21 0.0152 0.009
family Bacillaceae Control 21 0.0151 0.010
family Peptostreptococcaceae Control 0 0.0146 0.007
family Peptostreptococcaceae Treated 21 0.0136 0.005
family Carnobacteriaceae Treated 8 0.0135 0.007
family Bacillaceae Treated 21 0.0132 0.006
family Carnobacteriaceae Control 0 0.0132 0.008
family Carnobacteriaceae Treated 21 0.0132 0.007
family Carnobacteriaceae Treated 28 0.0132 0.006
family Carnobacteriaceae Control 8 0.0131 0.008
family Bacteroidaceae Control 8 0.0130 0.014
family Family XIII Control 0 0.0130 0.008
family Flavobacteriaceae Treated 21 0.0129 0.013
family Microbacteriaceae Control 21 0.0124 0.008
family Bacteroidaceae Treated 8 0.0121 0.005
family Sphingomonadaceae Control 8 0.0121 0.006
family Sphingomonadaceae Control 28 0.0121 0.009
family Lactobacillaceae Treated 28 0.0120 0.008
family Clostridiaceae 1 Treated 0 0.0119 0.007
family Shewanellaceae Control 28 0.0119 0.006
family Burkholderiaceae Control 8 0.0118 0.011
family Burkholderiaceae Treated 21 0.0118 0.008
family Sphingomonadaceae Treated 0 0.0118 0.014
family Xanthobacteraceae Control 21 0.0118 0.005
family Burkholderiaceae Treated 8 0.0117 0.006
family Christensenellaceae Control 21 0.0117 0.011
family Xanthomonadaceae Control 21 0.0117 0.005
family Rhizobiaceae Treated 8 0.0110 0.005
family Flavobacteriaceae Treated 0 0.0109 0.002
family Family XIII Treated 0 0.0108 0.004
family Bacteroidaceae Treated 28 0.0106 0.007
family Corynebacteriaceae Treated 21 0.0106 0.006
family Rhizobiaceae Control 0 0.0105 0.008
family Bacillaceae Control 8 0.0104 0.008
family Erysipelotrichaceae Control 8 0.0104 0.004
family Clostridiaceae 1 Control 8 0.0103 0.006
genus Pseudomonas Control 28 0.1405 0.065
genus Pseudomonas Control 21 0.0825 0.045
genus Cutibacterium Control 28 0.0734 0.028
genus Pseudomonas Treated 28 0.0671 0.071
genus Pseudomonas Control 8 0.0666 0.061
genus Methylobacterium Control 28 0.0603 0.033
genus Pseudomonas Treated 8 0.0592 0.055
genus Halomonas Control 28 0.0511 0.021
genus Pseudomonas Treated 0 0.0504 0.028
genus Pseudomonas Treated 21 0.0495 0.043
genus Ruminococcaceae UCG-010 Control 0 0.0459 0.025
genus Pseudomonas Control 0 0.0453 0.029
genus Cutibacterium Treated 28 0.0416 0.021
genus Methylobacterium Control 21 0.0401 0.022
genus Methylobacterium Control 8 0.0394 0.035
genus Ruminococcaceae UCG-005 Control 0 0.0393 0.020
genus Staphylococcus Control 8 0.0384 0.047
genus Staphylococcus Treated 8 0.0367 0.017
genus Cutibacterium Control 0 0.0365 0.027
genus Ruminococcaceae UCG-010 Treated 21 0.0362 0.023
genus Cutibacterium Control 21 0.0361 0.022
genus Cutibacterium Treated 0 0.0360 0.014
genus Ruminococcaceae UCG-005 Treated 21 0.0356 0.026
genus Ruminococcaceae UCG-010 Treated 0 0.0354 0.015
genus Cutibacterium Control 8 0.0350 0.022
genus Methylobacterium Treated 8 0.0349 0.027
genus Halomonas Control 21 0.0320 0.015
genus Halomonas Control 8 0.0313 0.024
genus Christensenellaceae R-7 group Control 0 0.0308 0.025
genus Cutibacterium Treated 8 0.0307 0.019
genus Ruminococcaceae UCG-005 Treated 0 0.0303 0.015
genus Halomonas Treated 28 0.0298 0.022
genus Streptococcus Control 8 0.0298 0.013
genus Ruminococcaceae UCG-010 Control 8 0.0295 0.018
genus Psychrobacter Treated 0 0.0292 0.010
genus Ruminococcaceae UCG-010 Treated 28 0.0291 0.013
genus Streptococcus Treated 28 0.0287 0.015
genus Ruminococcaceae UCG-005 Control 8 0.0286 0.026
genus Psychrobacter Treated 28 0.0283 0.007
genus Streptococcus Treated 0 0.0283 0.010
genus Ruminococcaceae UCG-010 Treated 8 0.0277 0.020
genus Methylobacterium Treated 28 0.0276 0.029
genus Staphylococcus Control 28 0.0272 0.020
genus Psychrobacter Control 8 0.0271 0.008
genus Christensenellaceae R-7 group Treated 0 0.0259 0.011
genus Streptococcus Control 0 0.0254 0.017
genus Halomonas Treated 8 0.0251 0.019
genus Psychrobacter Control 0 0.0249 0.014
genus Ruminococcaceae UCG-005 Treated 8 0.0244 0.013
genus Staphylococcus Treated 28 0.0243 0.012
genus Christensenellaceae R-7 group Treated 21 0.0241 0.015
genus Ruminococcaceae UCG-005 Treated 28 0.0241 0.007
genus Psychrobacter Control 28 0.0233 0.013
genus Streptococcus Treated 8 0.0233 0.011
genus Psychrobacter Treated 8 0.0232 0.008
genus Christensenellaceae R-7 group Control 8 0.0227 0.021
genus Staphylococcus Control 21 0.0224 0.017
genus Rikenellaceae RC9 gut group Treated 28 0.0223 0.010
genus Acinetobacter Control 28 0.0221 0.011
genus [Eubacterium] coprostanoligenes group Control 0 0.0219 0.009
genus Halomonas Treated 0 0.0219 0.008
genus Methylobacterium Treated 21 0.0219 0.022
genus Rikenellaceae RC9 gut group Treated 21 0.0219 0.011
genus Ruminococcaceae UCG-013 Control 0 0.0218 0.021
genus Prevotella 1 Treated 21 0.0217 0.011
genus Streptococcus Treated 21 0.0217 0.018
genus Rikenellaceae RC9 gut group Control 0 0.0213 0.008
genus Halomonas Treated 21 0.0212 0.015
genus Halomonas Control 0 0.0211 0.010
genus Cutibacterium Treated 21 0.0209 0.015
genus Rikenellaceae RC9 gut group Treated 0 0.0207 0.009
genus Bacteroides Control 0 0.0205 0.009
genus Psychrobacter Treated 21 0.0203 0.016
genus Christensenellaceae R-7 group Treated 28 0.0202 0.008
genus Prevotella 1 Control 28 0.0197 0.017
genus Prevotella 1 Control 8 0.0196 0.008
genus Methylobacterium Treated 0 0.0194 0.019
genus Staphylococcus Treated 21 0.0194 0.013
genus [Eubacterium] coprostanoligenes group Treated 21 0.0192 0.011
genus [Eubacterium] coprostanoligenes group Treated 0 0.0190 0.009
genus Staphylococcus Treated 0 0.0190 0.006
genus Staphylococcus Control 0 0.0189 0.011
genus Ruminococcaceae UCG-005 Control 21 0.0187 0.011
genus [Eubacterium] coprostanoligenes group Treated 28 0.0185 0.009
genus Methylobacterium Control 0 0.0184 0.014
genus Psychrobacter Control 21 0.0183 0.009
genus Ruminococcaceae UCG-010 Control 28 0.0177 0.016
genus Ruminococcaceae UCG-005 Control 28 0.0176 0.018
genus Streptococcus Control 28 0.0176 0.013
genus Rikenellaceae RC9 gut group Control 8 0.0174 0.007
genus [Eubacterium] coprostanoligenes group Treated 8 0.0169 0.008
genus Ruminococcaceae UCG-010 Control 21 0.0169 0.018
genus Christensenellaceae R-7 group Treated 8 0.0166 0.013
genus Bacteroides Treated 21 0.0165 0.010
genus Bacteroides Treated 0 0.0164 0.006
genus Prevotella 1 Treated 8 0.0164 0.007
genus Corynebacterium 1 Control 21 0.0163 0.010
genus Corynebacterium 1 Treated 8 0.0161 0.007
genus Prevotella 1 Control 21 0.0161 0.009
genus Ruminococcaceae UCG-013 Treated 21 0.0161 0.015
genus Prevotella 1 Treated 0 0.0157 0.008
genus Streptococcus Control 21 0.0157 0.010
genus Corynebacterium 1 Control 8 0.0154 0.012
genus Rikenellaceae RC9 gut group Treated 8 0.0148 0.008
genus Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium Control 28 0.0144 0.014
genus Prevotella 1 Control 0 0.0143 0.006
genus Prevotella 1 Treated 28 0.0140 0.004
genus Corynebacterium 1 Treated 0 0.0139 0.003
genus Ruminococcaceae UCG-014 Control 0 0.0138 0.012
genus Lachnospiraceae NK3A20 group Treated 0 0.0137 0.004
genus Bacillus Control 21 0.0136 0.009
genus Lachnospiraceae NK3A20 group Treated 8 0.0133 0.005
genus Corynebacterium 1 Treated 28 0.0132 0.007
genus Rikenellaceae RC9 gut group Control 28 0.0132 0.010
genus Bacteroides Control 8 0.0130 0.014
genus Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium Control 21 0.0125 0.011
genus Acinetobacter Treated 8 0.0123 0.014
genus Bacteroides Treated 8 0.0121 0.005
genus Lachnospiraceae NK3A20 group Control 0 0.0121 0.003
genus Corynebacterium 1 Control 28 0.0120 0.007
genus Flavobacterium Control 21 0.0120 0.012
genus Lactobacillus Treated 28 0.0120 0.008
genus Christensenellaceae R-7 group Control 21 0.0117 0.011
genus Lachnospiraceae NK3A20 group Treated 28 0.0117 0.007
genus Acinetobacter Treated 0 0.0116 0.004
genus Bacillus Treated 21 0.0116 0.005
genus Bacillus Treated 8 0.0113 0.007
genus Lachnospiraceae NK3A20 group Control 8 0.0113 0.006
genus Rikenellaceae RC9 gut group Control 21 0.0113 0.006
genus Sphingomonas Control 21 0.0113 0.008
genus Corynebacterium 1 Control 0 0.0112 0.008
genus [Eubacterium] coprostanoligenes group Control 8 0.0111 0.011
genus Acinetobacter Control 8 0.0110 0.005
genus Bacteroides Treated 28 0.0106 0.007
genus Shewanella Control 28 0.0106 0.005
genus Acinetobacter Treated 28 0.0105 0.005
genus Acinetobacter Control 21 0.0104 0.005
genus Clostridium sensu stricto 1 Treated 0 0.0104 0.006
genus [Eubacterium] coprostanoligenes group Control 21 0.0103 0.006
genus Achromobacter Control 28 0.0102 0.006
order Clostridiales Control 0 0.3586 0.158
order Clostridiales Treated 21 0.2907 0.161
order Clostridiales Treated 0 0.2875 0.092
order Clostridiales Control 8 0.2556 0.132
order Clostridiales Treated 28 0.2475 0.086
order Clostridiales Treated 8 0.2414 0.118
order Pseudomonadales Control 28 0.1931 0.065
order Clostridiales Control 21 0.1766 0.084
order Clostridiales Control 28 0.1437 0.102
order Bacteroidales Control 0 0.1207 0.024
order Bacteroidales Treated 21 0.1176 0.042
order Pseudomonadales Control 21 0.1169 0.051
order Pseudomonadales Treated 28 0.1128 0.075
order Bacteroidales Treated 0 0.1111 0.024
order Pseudomonadales Control 8 0.1074 0.067
order Rhizobiales Control 28 0.1032 0.054
order Bacteroidales Control 8 0.1028 0.024
order Bacteroidales Treated 28 0.0992 0.039
order Bacteroidales Treated 8 0.0977 0.034
order Pseudomonadales Treated 8 0.0956 0.063
order Pseudomonadales Treated 0 0.0948 0.031
order Rhizobiales Control 21 0.0853 0.041
order Pseudomonadales Control 0 0.0823 0.038
order Propionibacteriales Control 28 0.0811 0.029
order Pseudomonadales Treated 21 0.0773 0.051
order Bacteroidales Control 21 0.0700 0.018
order Bacillales Treated 8 0.0693 0.016
order Bacteroidales Control 28 0.0682 0.047
order Bacillales Control 8 0.0665 0.047
order Rhizobiales Treated 28 0.0619 0.048
order Rhizobiales Treated 8 0.0611 0.035
order Rhizobiales Control 8 0.0609 0.042
order Lactobacillales Treated 28 0.0604 0.018
order Lactobacillales Treated 0 0.0596 0.013
order Lactobacillales Control 8 0.0579 0.026
order Micrococcales Treated 8 0.0550 0.018
order Propionibacteriales Control 21 0.0550 0.018
order Oceanospirillales Control 28 0.0544 0.022
order Lactobacillales Treated 8 0.0534 0.017
order Micrococcales Control 21 0.0530 0.015
order Micrococcales Treated 0 0.0524 0.013
order Micrococcales Control 28 0.0519 0.022
order Micrococcales Treated 28 0.0506 0.017
order Lactobacillales Treated 21 0.0500 0.029
order Propionibacteriales Treated 28 0.0499 0.017
order Bacillales Control 21 0.0497 0.009
order Bacillales Control 28 0.0493 0.026
order Lactobacillales Control 0 0.0491 0.028
order Rhizobiales Treated 21 0.0484 0.030
order Bacillales Treated 28 0.0475 0.018
order Bacillales Treated 0 0.0465 0.014
order Bacillales Treated 21 0.0452 0.014
order Propionibacteriales Treated 0 0.0442 0.015
order Propionibacteriales Control 8 0.0431 0.020
order Micrococcales Control 8 0.0429 0.016
order Propionibacteriales Control 0 0.0427 0.028
order Propionibacteriales Treated 8 0.0409 0.019
order Micrococcales Treated 21 0.0401 0.022
order Micrococcales Control 0 0.0399 0.023
order Rhizobiales Control 0 0.0387 0.030
order Rhizobiales Treated 0 0.0384 0.029
order Lactobacillales Control 21 0.0380 0.018
order Bacillales Control 0 0.0374 0.017
order Lactobacillales Control 28 0.0363 0.025
order Oceanospirillales Control 21 0.0340 0.016
order Oceanospirillales Control 8 0.0331 0.024
order Corynebacteriales Control 21 0.0324 0.013
order Oceanospirillales Treated 28 0.0319 0.023
order Propionibacteriales Treated 21 0.0292 0.016
order Corynebacteriales Treated 8 0.0285 0.012
order Betaproteobacteriales Control 21 0.0279 0.013
order Oceanospirillales Treated 8 0.0278 0.020
order Corynebacteriales Treated 28 0.0270 0.008
order Corynebacteriales Control 28 0.0255 0.011
order Sphingomonadales Control 21 0.0253 0.012
order Corynebacteriales Control 8 0.0251 0.016
order Alteromonadales Control 28 0.0250 0.008
order Corynebacteriales Treated 0 0.0239 0.007
order Oceanospirillales Treated 0 0.0236 0.007
order Oceanospirillales Control 0 0.0225 0.010
order Oceanospirillales Treated 21 0.0225 0.016
order Flavobacteriales Control 21 0.0212 0.013
order Alteromonadales Treated 28 0.0209 0.006
order Alteromonadales Treated 0 0.0186 0.006
order Sphingomonadales Treated 8 0.0182 0.013
order Corynebacteriales Control 0 0.0176 0.011
order Betaproteobacteriales Control 28 0.0175 0.009
order Alteromonadales Control 8 0.0163 0.005
order Corynebacteriales Treated 21 0.0157 0.006
order Betaproteobacteriales Treated 21 0.0155 0.012
order Sphingomonadales Treated 21 0.0154 0.016
order Alteromonadales Control 0 0.0151 0.007
order Alteromonadales Treated 8 0.0151 0.008
order Flavobacteriales Treated 0 0.0151 0.002
order Flavobacteriales Treated 21 0.0149 0.015
order Alteromonadales Treated 21 0.0136 0.012
order Aeromonadales Treated 28 0.0131 0.004
order Alteromonadales Control 21 0.0129 0.006
order Betaproteobacteriales Control 8 0.0125 0.012
order Betaproteobacteriales Treated 8 0.0124 0.006
order Sphingomonadales Control 8 0.0121 0.006
order Sphingomonadales Control 28 0.0121 0.009
order Flavobacteriales Treated 28 0.0118 0.005
order Sphingomonadales Treated 0 0.0118 0.014
order Xanthomonadales Control 21 0.0118 0.005
order Flavobacteriales Control 0 0.0113 0.006
order Flavobacteriales Treated 8 0.0110 0.003
order Aeromonadales Treated 0 0.0109 0.004
order Erysipelotrichales Control 8 0.0104 0.004
order Aeromonadales Control 28 0.0103 0.004
order Aeromonadales Control 0 0.0102 0.006
order Betaproteobacteriales Treated 28 0.0101 0.009
phylum Firmicutes Control 0 0.4610 0.127
phylum Proteobacteria Control 28 0.4594 0.161
phylum Firmicutes Treated 0 0.4081 0.087
phylum Firmicutes Treated 21 0.4007 0.147
phylum Firmicutes Control 8 0.3945 0.129
phylum Firmicutes Treated 8 0.3781 0.123
phylum Firmicutes Treated 28 0.3689 0.108
phylum Proteobacteria Control 21 0.3559 0.111
phylum Proteobacteria Treated 28 0.3000 0.164
phylum Proteobacteria Control 8 0.2911 0.147
phylum Proteobacteria Treated 8 0.2855 0.147
phylum Firmicutes Control 21 0.2753 0.090
phylum Proteobacteria Treated 0 0.2507 0.079
phylum Proteobacteria Treated 21 0.2458 0.127
phylum Firmicutes Control 28 0.2414 0.119
phylum Proteobacteria Control 0 0.2176 0.104
phylum Actinobacteria Control 21 0.1785 0.029
phylum Actinobacteria Control 28 0.1785 0.045
phylum Actinobacteria Treated 8 0.1577 0.039
phylum Actinobacteria Treated 28 0.1540 0.021
phylum Bacteroidetes Treated 21 0.1487 0.025
phylum Actinobacteria Treated 0 0.1438 0.033
phylum Actinobacteria Control 8 0.1344 0.049
phylum Bacteroidetes Control 0 0.1341 0.023
phylum Bacteroidetes Treated 0 0.1308 0.021
phylum Actinobacteria Control 0 0.1225 0.059
phylum Actinobacteria Treated 21 0.1149 0.038
phylum Bacteroidetes Control 8 0.1148 0.026
phylum Bacteroidetes Treated 8 0.1147 0.035
phylum Bacteroidetes Treated 28 0.1135 0.044
phylum Bacteroidetes Control 21 0.1120 0.035
phylum Bacteroidetes Control 28 0.0766 0.050
phylum Cyanobacteria Treated 28 0.0146 0.003
phylum Acidobacteria Control 21 0.0142 0.009
phylum Acidobacteria Treated 21 0.0128 0.022
phylum Cyanobacteria Treated 0 0.0113 0.005
phylum Planctomycetes Treated 21 0.0103 0.018

##Class

Dclass <- D %>%
  filter(level=="class")

p <- ggplot(Dclass, aes(x=factor(1), y=avg_abund, fill=new_taxa)) + geom_bar(width=1,stat="identity", position = "fill")
p <- p + facet_grid(timepoint~treatment)
p <- p + guides(fill = guide_legend(title = "Class")) 
p <- p + geom_label_repel(aes(label = paste0(avg_abund*100, "%")), position=position_stack (vjust=0.5), size=4, show.legend = F)
my_palette = get_palette(c("green3","gold","blue","magenta","cyan","yellow","red","gray","purple", "darkorange1","pink1", "darkorchid1", "seagreen2"), length(unique(Dclass$new_taxa)))
p <- p + xlab("relative abundances") + ylab("percentages")
p <- p + scale_fill_manual(values = my_palette)
p <- p + theme(text = element_text(size=10),
               axis.text.x = element_text(size=8),
               # axis.text.y = element_text(size=4),
               strip.text = element_text(size = 8),
               axis.text.y = element_blank(),
               axis.ticks.y = element_blank(),
               legend.text=element_text(size=10),
               legend.title=element_text(size=10))
print(p)

#ggsave(p, height = 8, width = 8, filename ="taxonomy_class_bargraph_milk.png")

##Family

Dfamily <- D %>%
  filter(level=="family")

p <- ggplot(Dfamily, aes(x=factor(1), y=avg_abund, fill=new_taxa)) + geom_bar(width=1,stat="identity", position = "fill")
p <- p + facet_grid(timepoint~treatment)
p <- p + guides(fill = guide_legend(title = "Family")) 
#p <- p + geom_label_repel(aes(label = paste0(avg_abund*100, "%")), position=position_stack (vjust=0.5), size=4, show.legend = F)
my_palette2 = get_palette(c("green3","gold","blue","magenta","cyan","yellow","red","gray","purple","brown","black", "darkorange1","pink1", "darkorchid1", "seagreen2", "darkmagenta", "burlywood1", "maroon", "darkred", "burlywood3", "chartreuse4", "coral", "peachpuff", "mediumorchid3", "yellow3", "turquoise4", "snow", "slategray3", "orangered", "olivedrab", "plum", "lightcyan", "gray38", "forestgreen", "firebrick1"), length(unique(Dfamily$new_taxa)))
p <- p + xlab("relative abundances") + ylab("percentages")
p <- p + scale_fill_manual(values = my_palette2)
p <- p + theme(text = element_text(size=10),
               axis.text.x = element_text(size=8),
               # axis.text.y = element_text(size=4),
               strip.text = element_text(size = 8),
               axis.text.y = element_blank(),
               axis.ticks.y = element_blank(),
               legend.text=element_text(size=10),
               legend.title=element_text(size=10))
p

#ggsave(p, height = 8, width = 8, filename ="taxonomy_family_bargraph_MILK.png")

Genera

Dgenera <- D %>%
  filter(level=="genus")

p <- ggplot(Dgenera, aes(x=factor(1), y=avg_abund, fill=new_taxa)) + geom_bar(width=1,stat="identity", position = "fill")
p <- p + facet_grid(timepoint~treatment)
p <- p + guides(fill = guide_legend(title = "Genera")) 
my_palette2 = get_palette(c("green3","gold","blue","magenta","cyan","yellow","red","gray","purple","brown","black", "darkorange1","pink1", "darkorchid1", "seagreen2", "darkmagenta", "burlywood1", "maroon", "darkred", "burlywood3", "chartreuse4", "coral", "peachpuff", "mediumorchid3", "yellow3", "turquoise4", "snow", "slategray3", "orangered", "olivedrab", "plum", "lightcyan", "gray38", "forestgreen", "firebrick1"), length(unique(Dgenera$new_taxa)))
p <- p + xlab("relative abundances") + ylab("percentages")
p <- p + scale_fill_manual(values = my_palette2)
p <- p + theme(text = element_text(size=10),
               axis.text.x = element_text(size=8),
               # axis.text.y = element_text(size=4),
               strip.text = element_text(size = 8),
               axis.text.y = element_blank(),
               axis.ticks.y = element_blank(),
               legend.text=element_text(size=5),
               legend.title=element_text(size=5))
print(p)

#ggsave(p, height = 8, width = 8, filename ="taxonomy_genera_bargraph_MILK.png")

##Order

Dorder <- D %>%
  filter(level=="order")

p <- ggplot(Dorder, aes(x=factor(1), y=avg_abund, fill=new_taxa)) + geom_bar(width=1,stat="identity", position = "fill")
p <- p + facet_grid(timepoint~treatment)
p <- p + guides(fill = guide_legend(title = "Order")) 
my_palette2 = get_palette(c("red","darkred", "burlywood3", "chartreuse4","gray","gold","blue","magenta","cyan","purple","green3","yellow","brown","black", "darkorange1","pink1", "darkorchid1", "seagreen2", "darkmagenta", "burlywood1", "maroon",  "coral", "peachpuff", "mediumorchid3", "yellow3", "turquoise4", "snow", "slategray3", "orangered", "olivedrab", "plum", "lightcyan", "gray38", "forestgreen", "firebrick1"), length(unique(Dorder$new_taxa)))
p <- p + xlab("relative abundances") + ylab("percentages")
p <- p + scale_fill_manual(values = my_palette2)
p <- p + theme(text = element_text(size=10),
               axis.text.x = element_text(size=8),
               # axis.text.y = element_text(size=4),
               strip.text = element_text(size = 8),
               axis.text.y = element_blank(),
               axis.ticks.y = element_blank(),
               legend.text=element_text(size=10),
               legend.title=element_text(size=10))
print(p)

#ggsave(p, height = 8, width = 8, filename ="taxonomy_order_bargraph_MILK.png")

##Phylum

Dphylum <- D %>%
  filter(level=="phylum")

p <- ggplot(Dphylum, aes(x=factor(1), y=avg_abund, fill=new_taxa)) + geom_bar(width=1,stat="identity", position = "fill")
p <- p + facet_grid(timepoint~treatment)
p <- p + guides(fill = guide_legend(title = "Phylum")) 
p <- p + geom_label_repel(aes(label = paste0(avg_abund*100, "%")), position=position_stack (vjust=0.5), size=4, show.legend = F)
my_palette3 = get_palette(c("red", "green3","yellow","darkmagenta", "gray","lightcyan", "gold","blue"), length(unique(Dphylum$new_taxa)))
p <- p + xlab("relative abundances") + ylab("percentages")
p <- p + scale_fill_manual(values = my_palette3)
p <- p + theme(text = element_text(size=10),
               axis.text.x = element_text(size=8),
               # axis.text.y = element_text(size=4),
               strip.text = element_text(size = 8),
               axis.text.y = element_blank(),
               axis.ticks.y = element_blank(),
               legend.text=element_text(size=10),
               legend.title=element_text(size=10))
print(p)

#ggsave(p, height = 8, width = 8, filename ="taxonomy_phylum_bargraph_MILK.png")

Same results, but in wide-format (treatments on the horizontal axis): relative abundances (no standard deviations):

level new_taxa timepoint Control Treated
phylum Acidobacteria 21 0.0142 0.0128
phylum Actinobacteria 0 0.1225 0.1438
phylum Actinobacteria 8 0.1344 0.1577
phylum Actinobacteria 21 0.1785 0.1149
phylum Actinobacteria 28 0.1785 0.1540
phylum Bacteroidetes 0 0.1341 0.1308
phylum Bacteroidetes 8 0.1148 0.1147
phylum Bacteroidetes 21 0.1120 0.1487
phylum Bacteroidetes 28 0.0766 0.1135
phylum Cyanobacteria 0 NA 0.0113
phylum Cyanobacteria 28 NA 0.0146
phylum Firmicutes 0 0.4610 0.4081
phylum Firmicutes 8 0.3945 0.3781
phylum Firmicutes 21 0.2753 0.4007
phylum Firmicutes 28 0.2414 0.3689
phylum Planctomycetes 21 NA 0.0103
phylum Proteobacteria 0 0.2176 0.2507
phylum Proteobacteria 8 0.2911 0.2855
phylum Proteobacteria 21 0.3559 0.2458
phylum Proteobacteria 28 0.4594 0.3000
class Actinobacteria 0 0.1109 0.1334
class Actinobacteria 8 0.1237 0.1444
class Actinobacteria 21 0.1590 0.1008
class Actinobacteria 28 0.1734 0.1416
class Alphaproteobacteria 0 0.0599 0.0649
class Alphaproteobacteria 8 0.0915 0.0995
class Alphaproteobacteria 21 0.1331 0.0810
class Alphaproteobacteria 28 0.1358 0.0857
class Bacilli 0 0.0864 0.1061
class Bacilli 8 0.1244 0.1227
class Bacilli 21 0.0877 0.0952
class Bacilli 28 0.0856 0.1079
class Bacteroidia 0 0.1341 0.1308
class Bacteroidia 8 0.1148 0.1147
class Bacteroidia 21 0.1120 0.1487
class Bacteroidia 28 0.0766 0.1135
class Clostridia 0 0.3587 0.2875
class Clostridia 8 0.2556 0.2419
class Clostridia 21 0.1766 0.2907
class Clostridia 28 0.1438 0.2478
class Erysipelotrichia 8 0.0104 NA
class Gammaproteobacteria 0 0.1545 0.1826
class Gammaproteobacteria 8 0.1972 0.1801
class Gammaproteobacteria 21 0.2209 0.1602
class Gammaproteobacteria 28 0.3224 0.2116
order Aeromonadales 0 0.0102 0.0109
order Aeromonadales 28 0.0103 0.0131
order Alteromonadales 0 0.0151 0.0186
order Alteromonadales 8 0.0163 0.0151
order Alteromonadales 21 0.0129 0.0136
order Alteromonadales 28 0.0250 0.0209
order Bacillales 0 0.0374 0.0465
order Bacillales 8 0.0665 0.0693
order Bacillales 21 0.0497 0.0452
order Bacillales 28 0.0493 0.0475
order Bacteroidales 0 0.1207 0.1111
order Bacteroidales 8 0.1028 0.0977
order Bacteroidales 21 0.0700 0.1176
order Bacteroidales 28 0.0682 0.0992
order Betaproteobacteriales 8 0.0125 0.0124
order Betaproteobacteriales 21 0.0279 0.0155
order Betaproteobacteriales 28 0.0175 0.0101
order Clostridiales 0 0.3586 0.2875
order Clostridiales 8 0.2556 0.2414
order Clostridiales 21 0.1766 0.2907
order Clostridiales 28 0.1437 0.2475
order Corynebacteriales 0 0.0176 0.0239
order Corynebacteriales 8 0.0251 0.0285
order Corynebacteriales 21 0.0324 0.0157
order Corynebacteriales 28 0.0255 0.0270
order Erysipelotrichales 8 0.0104 NA
order Flavobacteriales 0 0.0113 0.0151
order Flavobacteriales 8 NA 0.0110
order Flavobacteriales 21 0.0212 0.0149
order Flavobacteriales 28 NA 0.0118
order Lactobacillales 0 0.0491 0.0596
order Lactobacillales 8 0.0579 0.0534
order Lactobacillales 21 0.0380 0.0500
order Lactobacillales 28 0.0363 0.0604
order Micrococcales 0 0.0399 0.0524
order Micrococcales 8 0.0429 0.0550
order Micrococcales 21 0.0530 0.0401
order Micrococcales 28 0.0519 0.0506
order Oceanospirillales 0 0.0225 0.0236
order Oceanospirillales 8 0.0331 0.0278
order Oceanospirillales 21 0.0340 0.0225
order Oceanospirillales 28 0.0544 0.0319
order Propionibacteriales 0 0.0427 0.0442
order Propionibacteriales 8 0.0431 0.0409
order Propionibacteriales 21 0.0550 0.0292
order Propionibacteriales 28 0.0811 0.0499
order Pseudomonadales 0 0.0823 0.0948
order Pseudomonadales 8 0.1074 0.0956
order Pseudomonadales 21 0.1169 0.0773
order Pseudomonadales 28 0.1931 0.1128
order Rhizobiales 0 0.0387 0.0384
order Rhizobiales 8 0.0609 0.0611
order Rhizobiales 21 0.0853 0.0484
order Rhizobiales 28 0.1032 0.0619
order Sphingomonadales 0 NA 0.0118
order Sphingomonadales 8 0.0121 0.0182
order Sphingomonadales 21 0.0253 0.0154
order Sphingomonadales 28 0.0121 NA
order Xanthomonadales 21 0.0118 NA
family Bacillaceae 8 0.0104 0.0159
family Bacillaceae 21 0.0151 0.0132
family Bacteroidaceae 0 0.0205 0.0164
family Bacteroidaceae 8 0.0130 0.0121
family Bacteroidaceae 21 NA 0.0165
family Bacteroidaceae 28 NA 0.0106
family Beijerinckiaceae 0 0.0236 0.0246
family Beijerinckiaceae 8 0.0459 0.0424
family Beijerinckiaceae 21 0.0453 0.0252
family Beijerinckiaceae 28 0.0675 0.0345
family Burkholderiaceae 8 0.0118 0.0117
family Burkholderiaceae 21 0.0230 0.0118
family Burkholderiaceae 28 0.0165 NA
family Carnobacteriaceae 0 0.0132 0.0178
family Carnobacteriaceae 8 0.0131 0.0135
family Carnobacteriaceae 21 NA 0.0132
family Carnobacteriaceae 28 NA 0.0132
family Christensenellaceae 0 0.0312 0.0261
family Christensenellaceae 8 0.0229 0.0166
family Christensenellaceae 21 0.0117 0.0242
family Christensenellaceae 28 NA 0.0202
family Clostridiaceae 1 0 NA 0.0119
family Clostridiaceae 1 8 0.0103 NA
family Corynebacteriaceae 0 0.0153 0.0194
family Corynebacteriaceae 8 0.0207 0.0214
family Corynebacteriaceae 21 0.0239 0.0106
family Corynebacteriaceae 28 0.0201 0.0190
family Erysipelotrichaceae 8 0.0104 NA
family Family XIII 0 0.0130 0.0108
family Flavobacteriaceae 0 NA 0.0109
family Flavobacteriaceae 21 0.0156 0.0129
family Halomonadaceae 0 0.0217 0.0226
family Halomonadaceae 8 0.0324 0.0258
family Halomonadaceae 21 0.0329 0.0216
family Halomonadaceae 28 0.0514 0.0303
family Lachnospiraceae 0 0.0734 0.0626
family Lachnospiraceae 8 0.0598 0.0558
family Lachnospiraceae 21 0.0423 0.0590
family Lachnospiraceae 28 0.0317 0.0582
family Lactobacillaceae 28 NA 0.0120
family Microbacteriaceae 21 0.0124 NA
family Micrococcaceae 0 0.0287 0.0348
family Micrococcaceae 8 0.0287 0.0338
family Micrococcaceae 21 0.0239 0.0235
family Micrococcaceae 28 0.0348 0.0352
family Moraxellaceae 0 0.0369 0.0441
family Moraxellaceae 8 0.0405 0.0363
family Moraxellaceae 21 0.0344 0.0275
family Moraxellaceae 28 0.0522 0.0456
family Nocardioidaceae 21 0.0154 NA
family Peptostreptococcaceae 0 0.0146 0.0187
family Peptostreptococcaceae 8 0.0159 0.0197
family Peptostreptococcaceae 21 0.0168 0.0136
family Peptostreptococcaceae 28 NA 0.0204
family Prevotellaceae 0 0.0354 0.0371
family Prevotellaceae 8 0.0364 0.0322
family Prevotellaceae 21 0.0260 0.0427
family Prevotellaceae 28 0.0272 0.0333
family Propionibacteriaceae 0 0.0379 0.0389
family Propionibacteriaceae 8 0.0379 0.0359
family Propionibacteriaceae 21 0.0396 0.0234
family Propionibacteriaceae 28 0.0759 0.0445
family Pseudomonadaceae 0 0.0454 0.0507
family Pseudomonadaceae 8 0.0668 0.0593
family Pseudomonadaceae 21 0.0825 0.0497
family Pseudomonadaceae 28 0.1409 0.0672
family Rhizobiaceae 0 0.0105 NA
family Rhizobiaceae 8 NA 0.0110
family Rhizobiaceae 21 0.0248 0.0152
family Rhizobiaceae 28 0.0268 0.0174
family Rikenellaceae 0 0.0345 0.0329
family Rikenellaceae 8 0.0256 0.0247
family Rikenellaceae 21 0.0173 0.0322
family Rikenellaceae 28 0.0188 0.0311
family Ruminococcaceae 0 0.2013 0.1397
family Ruminococcaceae 8 0.1210 0.1189
family Ruminococcaceae 21 0.0813 0.1613
family Ruminococcaceae 28 0.0757 0.1167
family Shewanellaceae 28 0.0119 NA
family Sphingomonadaceae 0 NA 0.0118
family Sphingomonadaceae 8 0.0121 0.0182
family Sphingomonadaceae 21 0.0253 0.0154
family Sphingomonadaceae 28 0.0121 NA
family Staphylococcaceae 0 0.0207 0.0224
family Staphylococcaceae 8 0.0438 0.0411
family Staphylococcaceae 21 0.0261 0.0228
family Staphylococcaceae 28 0.0316 0.0273
family Streptococcaceae 0 0.0256 0.0290
family Streptococcaceae 8 0.0299 0.0244
family Streptococcaceae 21 0.0161 0.0226
family Streptococcaceae 28 0.0181 0.0296
family Xanthobacteraceae 21 0.0118 NA
family Xanthomonadaceae 21 0.0117 NA
genus [Eubacterium] coprostanoligenes group 0 0.0219 0.0190
genus [Eubacterium] coprostanoligenes group 8 0.0111 0.0169
genus [Eubacterium] coprostanoligenes group 21 0.0103 0.0192
genus [Eubacterium] coprostanoligenes group 28 NA 0.0185
genus Achromobacter 28 0.0102 NA
genus Acinetobacter 0 NA 0.0116
genus Acinetobacter 8 0.0110 0.0123
genus Acinetobacter 21 0.0104 NA
genus Acinetobacter 28 0.0221 0.0105
genus Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium 21 0.0125 NA
genus Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium 28 0.0144 NA
genus Bacillus 8 NA 0.0113
genus Bacillus 21 0.0136 0.0116
genus Bacteroides 0 0.0205 0.0164
genus Bacteroides 8 0.0130 0.0121
genus Bacteroides 21 NA 0.0165
genus Bacteroides 28 NA 0.0106
genus Christensenellaceae R-7 group 0 0.0308 0.0259
genus Christensenellaceae R-7 group 8 0.0227 0.0166
genus Christensenellaceae R-7 group 21 0.0117 0.0241
genus Christensenellaceae R-7 group 28 NA 0.0202
genus Clostridium sensu stricto 1 0 NA 0.0104
genus Corynebacterium 1 0 0.0112 0.0139
genus Corynebacterium 1 8 0.0154 0.0161
genus Corynebacterium 1 21 0.0163 NA
genus Corynebacterium 1 28 0.0120 0.0132
genus Cutibacterium 0 0.0365 0.0360
genus Cutibacterium 8 0.0350 0.0307
genus Cutibacterium 21 0.0361 0.0209
genus Cutibacterium 28 0.0734 0.0416
genus Flavobacterium 21 0.0120 NA
genus Halomonas 0 0.0211 0.0219
genus Halomonas 8 0.0313 0.0251
genus Halomonas 21 0.0320 0.0212
genus Halomonas 28 0.0511 0.0298
genus Lachnospiraceae NK3A20 group 0 0.0121 0.0137
genus Lachnospiraceae NK3A20 group 8 0.0113 0.0133
genus Lachnospiraceae NK3A20 group 28 NA 0.0117
genus Lactobacillus 28 NA 0.0120
genus Methylobacterium 0 0.0184 0.0194
genus Methylobacterium 8 0.0394 0.0349
genus Methylobacterium 21 0.0401 0.0219
genus Methylobacterium 28 0.0603 0.0276
genus Prevotella 1 0 0.0143 0.0157
genus Prevotella 1 8 0.0196 0.0164
genus Prevotella 1 21 0.0161 0.0217
genus Prevotella 1 28 0.0197 0.0140
genus Pseudomonas 0 0.0453 0.0504
genus Pseudomonas 8 0.0666 0.0592
genus Pseudomonas 21 0.0825 0.0495
genus Pseudomonas 28 0.1405 0.0671
genus Psychrobacter 0 0.0249 0.0292
genus Psychrobacter 8 0.0271 0.0232
genus Psychrobacter 21 0.0183 0.0203
genus Psychrobacter 28 0.0233 0.0283
genus Rikenellaceae RC9 gut group 0 0.0213 0.0207
genus Rikenellaceae RC9 gut group 8 0.0174 0.0148
genus Rikenellaceae RC9 gut group 21 0.0113 0.0219
genus Rikenellaceae RC9 gut group 28 0.0132 0.0223
genus Ruminococcaceae UCG-005 0 0.0393 0.0303
genus Ruminococcaceae UCG-005 8 0.0286 0.0244
genus Ruminococcaceae UCG-005 21 0.0187 0.0356
genus Ruminococcaceae UCG-005 28 0.0176 0.0241
genus Ruminococcaceae UCG-010 0 0.0459 0.0354
genus Ruminococcaceae UCG-010 8 0.0295 0.0277
genus Ruminococcaceae UCG-010 21 0.0169 0.0362
genus Ruminococcaceae UCG-010 28 0.0177 0.0291
genus Ruminococcaceae UCG-013 0 0.0218 NA
genus Ruminococcaceae UCG-013 21 NA 0.0161
genus Ruminococcaceae UCG-014 0 0.0138 NA
genus Shewanella 28 0.0106 NA
genus Sphingomonas 21 0.0113 NA
genus Staphylococcus 0 0.0189 0.0190
genus Staphylococcus 8 0.0384 0.0367
genus Staphylococcus 21 0.0224 0.0194
genus Staphylococcus 28 0.0272 0.0243
genus Streptococcus 0 0.0254 0.0283
genus Streptococcus 8 0.0298 0.0233
genus Streptococcus 21 0.0157 0.0217
genus Streptococcus 28 0.0176 0.0287

timepoint

level new_taxa treatment 0 8 21 28
phylum Acidobacteria Control NA NA 0.0142 NA
phylum Acidobacteria Treated NA NA 0.0128 NA
phylum Actinobacteria Control 0.1225 0.1344 0.1785 0.1785
phylum Actinobacteria Treated 0.1438 0.1577 0.1149 0.1540
phylum Bacteroidetes Control 0.1341 0.1148 0.1120 0.0766
phylum Bacteroidetes Treated 0.1308 0.1147 0.1487 0.1135
phylum Cyanobacteria Treated 0.0113 NA NA 0.0146
phylum Firmicutes Control 0.4610 0.3945 0.2753 0.2414
phylum Firmicutes Treated 0.4081 0.3781 0.4007 0.3689
phylum Planctomycetes Treated NA NA 0.0103 NA
phylum Proteobacteria Control 0.2176 0.2911 0.3559 0.4594
phylum Proteobacteria Treated 0.2507 0.2855 0.2458 0.3000
class Actinobacteria Control 0.1109 0.1237 0.1590 0.1734
class Actinobacteria Treated 0.1334 0.1444 0.1008 0.1416
class Alphaproteobacteria Control 0.0599 0.0915 0.1331 0.1358
class Alphaproteobacteria Treated 0.0649 0.0995 0.0810 0.0857
class Bacilli Control 0.0864 0.1244 0.0877 0.0856
class Bacilli Treated 0.1061 0.1227 0.0952 0.1079
class Bacteroidia Control 0.1341 0.1148 0.1120 0.0766
class Bacteroidia Treated 0.1308 0.1147 0.1487 0.1135
class Clostridia Control 0.3587 0.2556 0.1766 0.1438
class Clostridia Treated 0.2875 0.2419 0.2907 0.2478
class Erysipelotrichia Control NA 0.0104 NA NA
class Gammaproteobacteria Control 0.1545 0.1972 0.2209 0.3224
class Gammaproteobacteria Treated 0.1826 0.1801 0.1602 0.2116
order Aeromonadales Control 0.0102 NA NA 0.0103
order Aeromonadales Treated 0.0109 NA NA 0.0131
order Alteromonadales Control 0.0151 0.0163 0.0129 0.0250
order Alteromonadales Treated 0.0186 0.0151 0.0136 0.0209
order Bacillales Control 0.0374 0.0665 0.0497 0.0493
order Bacillales Treated 0.0465 0.0693 0.0452 0.0475
order Bacteroidales Control 0.1207 0.1028 0.0700 0.0682
order Bacteroidales Treated 0.1111 0.0977 0.1176 0.0992
order Betaproteobacteriales Control NA 0.0125 0.0279 0.0175
order Betaproteobacteriales Treated NA 0.0124 0.0155 0.0101
order Clostridiales Control 0.3586 0.2556 0.1766 0.1437
order Clostridiales Treated 0.2875 0.2414 0.2907 0.2475
order Corynebacteriales Control 0.0176 0.0251 0.0324 0.0255
order Corynebacteriales Treated 0.0239 0.0285 0.0157 0.0270
order Erysipelotrichales Control NA 0.0104 NA NA
order Flavobacteriales Control 0.0113 NA 0.0212 NA
order Flavobacteriales Treated 0.0151 0.0110 0.0149 0.0118
order Lactobacillales Control 0.0491 0.0579 0.0380 0.0363
order Lactobacillales Treated 0.0596 0.0534 0.0500 0.0604
order Micrococcales Control 0.0399 0.0429 0.0530 0.0519
order Micrococcales Treated 0.0524 0.0550 0.0401 0.0506
order Oceanospirillales Control 0.0225 0.0331 0.0340 0.0544
order Oceanospirillales Treated 0.0236 0.0278 0.0225 0.0319
order Propionibacteriales Control 0.0427 0.0431 0.0550 0.0811
order Propionibacteriales Treated 0.0442 0.0409 0.0292 0.0499
order Pseudomonadales Control 0.0823 0.1074 0.1169 0.1931
order Pseudomonadales Treated 0.0948 0.0956 0.0773 0.1128
order Rhizobiales Control 0.0387 0.0609 0.0853 0.1032
order Rhizobiales Treated 0.0384 0.0611 0.0484 0.0619
order Sphingomonadales Control NA 0.0121 0.0253 0.0121
order Sphingomonadales Treated 0.0118 0.0182 0.0154 NA
order Xanthomonadales Control NA NA 0.0118 NA
family Bacillaceae Control NA 0.0104 0.0151 NA
family Bacillaceae Treated NA 0.0159 0.0132 NA
family Bacteroidaceae Control 0.0205 0.0130 NA NA
family Bacteroidaceae Treated 0.0164 0.0121 0.0165 0.0106
family Beijerinckiaceae Control 0.0236 0.0459 0.0453 0.0675
family Beijerinckiaceae Treated 0.0246 0.0424 0.0252 0.0345
family Burkholderiaceae Control NA 0.0118 0.0230 0.0165
family Burkholderiaceae Treated NA 0.0117 0.0118 NA
family Carnobacteriaceae Control 0.0132 0.0131 NA NA
family Carnobacteriaceae Treated 0.0178 0.0135 0.0132 0.0132
family Christensenellaceae Control 0.0312 0.0229 0.0117 NA
family Christensenellaceae Treated 0.0261 0.0166 0.0242 0.0202
family Clostridiaceae 1 Control NA 0.0103 NA NA
family Clostridiaceae 1 Treated 0.0119 NA NA NA
family Corynebacteriaceae Control 0.0153 0.0207 0.0239 0.0201
family Corynebacteriaceae Treated 0.0194 0.0214 0.0106 0.0190
family Erysipelotrichaceae Control NA 0.0104 NA NA
family Family XIII Control 0.0130 NA NA NA
family Family XIII Treated 0.0108 NA NA NA
family Flavobacteriaceae Control NA NA 0.0156 NA
family Flavobacteriaceae Treated 0.0109 NA 0.0129 NA
family Halomonadaceae Control 0.0217 0.0324 0.0329 0.0514
family Halomonadaceae Treated 0.0226 0.0258 0.0216 0.0303
family Lachnospiraceae Control 0.0734 0.0598 0.0423 0.0317
family Lachnospiraceae Treated 0.0626 0.0558 0.0590 0.0582
family Lactobacillaceae Treated NA NA NA 0.0120
family Microbacteriaceae Control NA NA 0.0124 NA
family Micrococcaceae Control 0.0287 0.0287 0.0239 0.0348
family Micrococcaceae Treated 0.0348 0.0338 0.0235 0.0352
family Moraxellaceae Control 0.0369 0.0405 0.0344 0.0522
family Moraxellaceae Treated 0.0441 0.0363 0.0275 0.0456
family Nocardioidaceae Control NA NA 0.0154 NA
family Peptostreptococcaceae Control 0.0146 0.0159 0.0168 NA
family Peptostreptococcaceae Treated 0.0187 0.0197 0.0136 0.0204
family Prevotellaceae Control 0.0354 0.0364 0.0260 0.0272
family Prevotellaceae Treated 0.0371 0.0322 0.0427 0.0333
family Propionibacteriaceae Control 0.0379 0.0379 0.0396 0.0759
family Propionibacteriaceae Treated 0.0389 0.0359 0.0234 0.0445
family Pseudomonadaceae Control 0.0454 0.0668 0.0825 0.1409
family Pseudomonadaceae Treated 0.0507 0.0593 0.0497 0.0672
family Rhizobiaceae Control 0.0105 NA 0.0248 0.0268
family Rhizobiaceae Treated NA 0.0110 0.0152 0.0174
family Rikenellaceae Control 0.0345 0.0256 0.0173 0.0188
family Rikenellaceae Treated 0.0329 0.0247 0.0322 0.0311
family Ruminococcaceae Control 0.2013 0.1210 0.0813 0.0757
family Ruminococcaceae Treated 0.1397 0.1189 0.1613 0.1167
family Shewanellaceae Control NA NA NA 0.0119
family Sphingomonadaceae Control NA 0.0121 0.0253 0.0121
family Sphingomonadaceae Treated 0.0118 0.0182 0.0154 NA
family Staphylococcaceae Control 0.0207 0.0438 0.0261 0.0316
family Staphylococcaceae Treated 0.0224 0.0411 0.0228 0.0273
family Streptococcaceae Control 0.0256 0.0299 0.0161 0.0181
family Streptococcaceae Treated 0.0290 0.0244 0.0226 0.0296
family Xanthobacteraceae Control NA NA 0.0118 NA
family Xanthomonadaceae Control NA NA 0.0117 NA
genus [Eubacterium] coprostanoligenes group Control 0.0219 0.0111 0.0103 NA
genus [Eubacterium] coprostanoligenes group Treated 0.0190 0.0169 0.0192 0.0185
genus Achromobacter Control NA NA NA 0.0102
genus Acinetobacter Control NA 0.0110 0.0104 0.0221
genus Acinetobacter Treated 0.0116 0.0123 NA 0.0105
genus Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium Control NA NA 0.0125 0.0144
genus Bacillus Control NA NA 0.0136 NA
genus Bacillus Treated NA 0.0113 0.0116 NA
genus Bacteroides Control 0.0205 0.0130 NA NA
genus Bacteroides Treated 0.0164 0.0121 0.0165 0.0106
genus Christensenellaceae R-7 group Control 0.0308 0.0227 0.0117 NA
genus Christensenellaceae R-7 group Treated 0.0259 0.0166 0.0241 0.0202
genus Clostridium sensu stricto 1 Treated 0.0104 NA NA NA
genus Corynebacterium 1 Control 0.0112 0.0154 0.0163 0.0120
genus Corynebacterium 1 Treated 0.0139 0.0161 NA 0.0132
genus Cutibacterium Control 0.0365 0.0350 0.0361 0.0734
genus Cutibacterium Treated 0.0360 0.0307 0.0209 0.0416
genus Flavobacterium Control NA NA 0.0120 NA
genus Halomonas Control 0.0211 0.0313 0.0320 0.0511
genus Halomonas Treated 0.0219 0.0251 0.0212 0.0298
genus Lachnospiraceae NK3A20 group Control 0.0121 0.0113 NA NA
genus Lachnospiraceae NK3A20 group Treated 0.0137 0.0133 NA 0.0117
genus Lactobacillus Treated NA NA NA 0.0120
genus Methylobacterium Control 0.0184 0.0394 0.0401 0.0603
genus Methylobacterium Treated 0.0194 0.0349 0.0219 0.0276
genus Prevotella 1 Control 0.0143 0.0196 0.0161 0.0197
genus Prevotella 1 Treated 0.0157 0.0164 0.0217 0.0140
genus Pseudomonas Control 0.0453 0.0666 0.0825 0.1405
genus Pseudomonas Treated 0.0504 0.0592 0.0495 0.0671
genus Psychrobacter Control 0.0249 0.0271 0.0183 0.0233
genus Psychrobacter Treated 0.0292 0.0232 0.0203 0.0283
genus Rikenellaceae RC9 gut group Control 0.0213 0.0174 0.0113 0.0132
genus Rikenellaceae RC9 gut group Treated 0.0207 0.0148 0.0219 0.0223
genus Ruminococcaceae UCG-005 Control 0.0393 0.0286 0.0187 0.0176
genus Ruminococcaceae UCG-005 Treated 0.0303 0.0244 0.0356 0.0241
genus Ruminococcaceae UCG-010 Control 0.0459 0.0295 0.0169 0.0177
genus Ruminococcaceae UCG-010 Treated 0.0354 0.0277 0.0362 0.0291
genus Ruminococcaceae UCG-013 Control 0.0218 NA NA NA
genus Ruminococcaceae UCG-013 Treated NA NA 0.0161 NA
genus Ruminococcaceae UCG-014 Control 0.0138 NA NA NA
genus Shewanella Control NA NA NA 0.0106
genus Sphingomonas Control NA NA 0.0113 NA
genus Staphylococcus Control 0.0189 0.0384 0.0224 0.0272
genus Staphylococcus Treated 0.0190 0.0367 0.0194 0.0243
genus Streptococcus Control 0.0254 0.0298 0.0157 0.0176
genus Streptococcus Treated 0.0283 0.0233 0.0217 0.0287

Finally,a bubble chart to visualize relative abundances per taxa and treatment:

## `summarise()` has grouped output by 'level', 'new_taxa'. You can override using the `.groups` argument.

Significance of treatments (+ timepoint)

The significance of differences between treatments (Control vs Treated with Essential Oil) was evaluated using a linear model (ANOVA) that included the effect of timepoints:

\[ counts_{ikj} = \mu + timepoint_k + treatment_j + e_{ikj} \]

This way, the variability due to region is removed when assessing the effect of treatments.

Significance of treatments (per timepoint)

The significance of differences between treatments (Control vs Treated with Essential Oil) was evaluated using a linear model (ANOVA) that included the effect of timepoints:

\[ counts_{ij} = \mu + treatment_j + e_{ij} \]

this way, the variability due to region is removed when assessing the effect of treatments.

## `summarise()` has grouped output by 'level', 'new_taxa', 'timepoint'. You can override using the `.groups` argument.
## # A tibble: 5 × 2
##   level    tot
##   <chr>  <dbl>
## 1 class   4.00
## 2 family  3.89
## 3 genus   3.60
## 4 order   3.99
## 5 phylum  4
# dd_counts$type <- c("ileum","rumen")[match(dd_counts$type,unique(dd_counts$type))]
# dd <- bind_rows(dd_rumen, dd_ileal)
# dd <- dd_counts %>% inner_join(dd, by = c("level" = "level", "new_taxa" = "new_taxa", "type" = "type"))
# dd %>% fwrite("significant_otus_relabund.csv", sep=",")
DX <- D %>%
  filter(`p.value` <= 0.05) %>%
  select(c(level,new_taxa,timepoint,`p.value`)) %>%
  arrange(level,`p.value`)

D0 <- mO %>%
  dplyr::group_by(level,new_taxa,timepoint,treatment) %>%
  dplyr::summarise(avg_counts = mean(counts))
## `summarise()` has grouped output by 'level', 'new_taxa', 'timepoint'. You can override using the `.groups` argument.
to_save = list(D,DX,D0)
save(to_save, file = "taxonomy_timepoint.RData")

load("taxonomy_timepoint.RData")
D <- to_save[[1]]
DX <- to_save[[2]]
D0 <- to_save[[3]]

dd <- spread(D0, key = treatment, value = avg_counts)
temp <- inner_join(DX,dd, by = c("level" = "level", "new_taxa" = "new_taxa", "timepoint" = "timepoint"))
fwrite(temp, file = "significant_otus.csv", col.names = TRUE, sep = ",")
print (dd)
## # A tibble: 5,472 × 5
## # Groups:   level, new_taxa, timepoint [5,472]
##    level new_taxa       timepoint Control Treated
##    <chr> <chr>          <fct>       <dbl>   <dbl>
##  1 class Acidimicrobiia 0           7.72    7.26 
##  2 class Acidimicrobiia 8           5.78    7.18 
##  3 class Acidimicrobiia 21         17.2    14.6  
##  4 class Acidimicrobiia 28          4.31    7.17 
##  5 class Acidobacteriia 0           0.145   0.175
##  6 class Acidobacteriia 8           2.41    4.64 
##  7 class Acidobacteriia 21          7.88    4.46 
##  8 class Acidobacteriia 28          2.41    0.302
##  9 class Actinobacteria 0         293.    379.   
## 10 class Actinobacteria 8         276.    335.   
## # … with 5,462 more rows
load("taxonomy_timepoint.RData")
D <- to_save[[1]]
DX <- to_save[[2]]
D0 <- to_save[[3]]

D0 <- mutate(D0, avg_counts = avg_counts+1) %>% spread(key = treatment, value = avg_counts)

D1 <- DX %>%
  inner_join(D0, by = c("level" = "level", "new_taxa" = "new_taxa", "timepoint" = "timepoint")) %>%
  mutate(p.value = -log10(p.value), Control = ifelse(log(Control) < 0,0,log10(Control)), Treated = ifelse(log(Treated) < 0, 0, log10(Treated))) %>%
  gather(key = "treatment", value = "counts", -c(level,new_taxa,timepoint,p.value))

D1$level <- factor(D1$level, levels = c("phylum","class","order","family","genus"))

p <- ggplot(D1, aes(x = treatment, y = new_taxa, group=level))
p <- p + geom_tile(aes(fill = counts), colour = "white")
p <- p + facet_grid(level~timepoint, space="free", scales = "free_y")
p <- p + scale_fill_gradient(low = "orange", high = "blue")
p <- p + theme(strip.text.y = element_text(size = 5), 
               strip.text.x = element_text(size = 6),
               # axis.text.y = element_text(size = 4),
               axis.text.x = element_text(size = 6),
               axis.title = element_text(size = 6))
p <- p + guides(fill=FALSE) + theme(axis.title.y = element_blank(),
                                    axis.text.y = element_blank(),
                                    axis.ticks.y = element_blank())
## Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> =
## "none")` instead.
# p
dd <- filter(D1, treatment == "Control") %>% mutate(variable = "p-value")

q <- ggplot(dd, aes(x = factor(1), y = new_taxa, group=level))
q <- q + geom_tile(aes(fill = p.value), colour = "white")
q <- q + facet_grid(level~variable, space="free", scales = "free_y")
q <- q + scale_fill_gradient(low = "orange", high = "blue")
q <- q + theme(strip.text = element_text(size = 4), 
               strip.text.x = element_text(size = 6),
               axis.text.y = element_text(size = 5),
               axis.title = element_text(size = 6))
q <- q + guides(fill=FALSE) + theme(
  # axis.title.x = element_blank(),
  # axis.text.x=element_blank(),
  # axis.ticks.x=element_blank(),
  strip.text.y = element_blank(),
  # axis.text.x = element_blank()
  axis.text.x = element_text(size = 6)
)
## Warning: `guides(<scale> = FALSE)` is deprecated. Please use `guides(<scale> =
## "none")` instead.
q <- q + xlab("") 

figure_final <- ggarrange(q, p, widths=c(0.25, 0.75), 
                          labels=c("A", "B"))

print(figure_final)

#ggsave(filename = "heatmap_MILK.png", plot = figure_final, device = "png", width = 8, height = 10)